Hi All,

I am using homer annotatePeaks.pl (version 4.11) by providing the bed file. Surprisingly, in the output file all peaks start position is increasing by +1, while the end remains same as in the input bed file. I read through homer annotatePeaks.pl help page but not finding any reason specific to this context.

"Command used":

annotatePeaks.pl  Tumor_vs_Normal_peak_annotation_input_file.bed  hg38  -annStats  Tumor_vs_Normal_peaks_stats.txt  -CpG   -go GO_analysis_results   -genomeOntology   genome_ontology_results  >Tumor_vs_Normal_homer_annotation_output.txt"

Input file: tail Tumor_vs_Normal_peak_annotation_input_file.bed

chrM    10857   11082   peak_677899

chrM    13955   14612   peak_677900

As we seen in output file chr start site is. 13955 and 10857.

"Output file (only first few columns are shown):" tail Tumor_vs_Normal_homer_annotation_output.txt

peak_677899 chrM    10858   11082   +   0    NA      Intergenic ncRNA   0.013393    0.417778

peak_677900 chrM    13956   14612   +   0    NA  Intergenic ncRNA   0.013720    0.429224

As we seen in output file chr start site is. 13956 and 10858.

I do understand that annotation tools can be 0 and 1-based. But is there a way to retain peaks regions similar to input bed file? or I need to subtract 1 from all entries in that column?

Thanks

Rakesh